NM_005476.7(GNE):c.1583T>G (p.Phe528Cys) AND GNE myopathy

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Mar 26, 2024
Review status:: criteria provided, conflicting classifications

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000671522.4

Allele description [Variation Report for NM_005476.7(GNE):c.1583T>G (p.Phe528Cys)]

NM_005476.7(GNE):c.1583T>G (p.Phe528Cys)

Gene:

GNE:glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9p13.3

Genomic location:

Preferred name:

NM_005476.7(GNE):c.1583T>G (p.Phe528Cys)

HGVS:

NC_000009.12:g.36222827A>C
NG_008246.1:g.59218T>G
NM_001128227.3:c.1676T>G
NM_001190383.3:c.1411+546T>G
NM_001190384.3:c.1253T>G
NM_001190388.2:c.1406T>G
NM_001374797.1:c.1430T>G
NM_001374798.1:c.1406T>G
NM_005476.7:c.1583T>GMANE SELECT
NP_001121699.1:p.Phe559Cys
NP_001177313.1:p.Phe418Cys
NP_001177317.2:p.Phe469Cys
NP_001361726.1:p.Phe477Cys
NP_001361727.1:p.Phe469Cys
NP_005467.1:p.Phe528Cys
LRG_1197t1:c.1676T>G
LRG_1197t2:c.1583T>G
LRG_1197:g.59218T>G
LRG_1197p1:p.Phe559Cys
LRG_1197p2:p.Phe528Cys
NC_000009.11:g.36222824A>C
NM_001128227.2:c.1676T>G

Protein change:

F418C

Links:

dbSNP: rs986773986

NCBI 1000 Genomes Browser:

rs986773986

Molecular consequence:

NM_001190383.3:c.1411+546T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001128227.3:c.1676T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001190384.3:c.1253T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001190388.2:c.1406T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374797.1:c.1430T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374798.1:c.1406T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_005476.7:c.1583T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: GNE myopathy (NM)
Synonyms:: Nonaka myopathy; Nonaka distal myopathy; INCLUSION BODY MYOPATHY, HEREDITARY, AUTOSOMAL RECESSIVE; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0011603; MedGen: C1853926; Orphanet: 602; OMIM: 605820

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ODDD (1)
MeSH
olean-11,13(18)-diene-3,30-diol dihemiphthalate, disodium salt [Supplementary Co...
olean-11,13(18)-diene-3,30-diol dihemiphthalate, disodium salt [Supplementary Concept]
structure given in first source; RN given refers to (3beta,20beta)-isomer<br/>Date introduced: September 4, 1990<br/>

MeSH

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000796506	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Uncertain significance (Dec 27, 2017)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 12497639, 16503651 Citation Link,
SCV004199390	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 26, 2024)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000796506

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Uncertain significance
(Dec 27, 2017)

unknown

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link,

SCV004199390

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 26, 2024)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutations spectrum of GNE in hereditary inclusion body myopathy sparing the quadriceps.

Eisenberg I, Grabov-Nardini G, Hochner H, Korner M, Sadeh M, Bertorini T, Bushby K, Castellan C, Felice K, Mendell J, Merlini L, Shilling C, Wirguin I, Argov Z, Mitrani-Rosenbaum S.

Hum Mutat. 2003 Jan;21(1):99.

PubMed [citation]

PMID:: 12497639

Influence of UDP-GlcNAc 2-epimerase/ManNAc kinase mutant proteins on hereditary inclusion body myopathy.

Penner J, Mantey LR, Elgavish S, Ghaderi D, Cirak S, Berger M, Krause S, Lucka L, Voit T, Mitrani-Rosenbaum S, Hinderlich S.

Biochemistry. 2006 Mar 7;45(9):2968-77.

PubMed [citation]

PMID:: 16503651

See all PubMed Citations (3)

Details of each submission

From Counsyl, SCV000796506.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV004199390.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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